scholarly journals Investigation on Anthrax in Bangladesh during the Outbreaks of 2011 and Definition of the Epidemiological Correlations

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 481
Author(s):  
Domenico Galante ◽  
Viviana Manzulli ◽  
Luigina Serrecchia ◽  
Pietro Di Taranto ◽  
Martin Hugh-Jones ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Tandem Repeats ◽  
Animal Feed ◽  
Variable Number ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Major Lineage ◽  
Different Types ◽  
Definition Of ◽  
Nucleotide Repeats

In 2011, in Bangladesh, 11 anthrax outbreaks occurred in six districts of the country. Different types of samples were collected from May to September in the six districts where anthrax had occurred in order to detect and type Bacillus anthracis (B. anthracis) strains. Anthrax was detected in 46.6% of the samples analysed, in particular in soils, but also in bone samples, water, animal feed, and rumen ingesta of dead animals. Canonical single nucleotide polymorphisms (CanSNPs) analysis showed that all the isolates belonged to the major lineage A, sublineage A.Br.001/002 of China and Southeast Asia while the multi-locus variable number of tandem repeats (VNTRs) analysis (MLVA) with 15 VNTRs demonstrated the presence of five genotypes, of which two resulted to be new genotypes. The single nucleotide repeats (SNRs) analysis showed 13 SNR types; nevertheless, due to its higher discriminatory power, the presence of two isolates with different SNR-type polymorphisms was detected within two MLVA genotypes. This study assumes that soil is not the only reason for the spread of the disease in Bangladesh; contaminated feed and water can also play an important role in the epidemiology of anthrax. Possible explanations for these epidemiological relationships are discussed.

scholarly journals Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen

2006 ◽  
Vol 188 (12) ◽  
pp. 4453-4463 ◽  
Author(s):  
Patrick S. G. Chain ◽  
Ping Hu ◽  
Stephanie A. Malfatti ◽  
Lyndsay Radnedge ◽  
Frank Larimer ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Yersinia Pestis ◽  
Yersinia Pseudotuberculosis ◽  
Open Reading Frames ◽  
Genomic Diversity ◽  
Avirulent Strain ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Definition Of

ABSTRACT Yersinia pestis, the causative agent of bubonic and pneumonic plagues, has undergone detailed study at the molecular level. To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the “classical” antiqua biovar, strains Antiqua and Nepal516. The genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956 open reading frames, respectively. Though both strains belong to one of the three classical biovars, they represent separate lineages defined by recent phylogenetic studies. We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis. There are strain-specific rearrangements, insertions, deletions, single nucleotide polymorphisms, and a unique distribution of insertion sequences. We found 453 single nucleotide polymorphisms in protein-coding regions, which were used to assess the evolutionary relationships of these Y. pestis strains. Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. The results presented here clearly demonstrate the differences between the two biovar antiqua lineages and support the notion that grouping Y. pestis strains based strictly on the classical definition of biovars (predicated upon two biochemical assays) does not accurately reflect the phylogenetic relationships within this species. A comparison of four virulent Y. pestis strains with the human-avirulent strain 91001 provides further insight into the genetic basis of virulence to humans.

scholarly journals Comprehensive Insights Into Forensic Features and Genetic Background of Chinese Northwest Hui Group Using Six Distinct Categories of 231 Molecular Markers

2021 ◽  
Vol 12 ◽  
Author(s):  
Chong Chen ◽  
Xiaoye Jin ◽  
Xingru Zhang ◽  
Wenqing Zhang ◽  
Yuxin Guo ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Background ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Genetic Relationships ◽  
Population Data ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Short Tandem

The Hui minority is predominantly composed of Chinese-speaking Islamic adherents distributed throughout China, of which the individuals are mainly concentrated in Northwest China. In the present study, we employed the length and sequence polymorphisms-based typing system of 231 molecular markers, i.e., amelogenin, 22 phenotypic-informative single nucleotide polymorphisms (PISNPs), 94 identity-informative single nucleotide polymorphisms (IISNPs), 24 Y-chromosomal short tandem repeats (Y-STRs), 56 ancestry-informative single nucleotide polymorphisms (AISNPs), 7 X-chromosomal short tandem repeats (X-STRs), and 27 autosomal short tandem repeats (A-STRs), into 90 unrelated male individuals from the Chinese Northwest Hui group to comprehensively explore its forensic characteristics and genetic background. Total of 451 length-based and 652 sequence-based distinct alleles were identified from 58 short tandem repeats (STRs) in 90 unrelated Northwest Hui individuals, denoting that the sequence-based genetic markers could pronouncedly provide more genetic information than length-based markers. The forensic characteristics and efficiencies of STRs and IISNPs were estimated, both of which externalized high polymorphisms in the Northwest Hui group and could be further utilized in forensic investigations. No significant departure from the Hardy–Weinberg equilibrium (HWE) expectation was observed after the Bonferroni correction. Additionally, four group sets of reference population data were exploited to dissect the genetic background of the Northwest Hui group separately from different perspectives, which contained 26 populations for 93 IISNPs, 58 populations for 17 Y-STRs, 26 populations for 55 AISNPs (raw data), and 109 populations for 55 AISNPs (allele frequencies). As a result, the analyses based on the Y-STRs indicated that the Northwest Hui group primarily exhibited intimate genetic relationships with reference Hui groups from Chinese different regions except for the Sichuan Hui group and secondarily displayed close genetic relationships with populations from Central and West Asia, as well as several Chinese groups. However, the AISNP analyses demonstrated that the Northwest Hui group shared more intimate relationships with current East Asian populations apart from reference Hui group, harboring the large proportion of ancestral component contributed by East Asia.

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